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Carson et al. A Digital Atlas for the Mouse Brain Transcriptome
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A Digital Atlas to Characterize the Mouse Brain
Transcriptome
James P. Carson1,2*, Tao Ju3, Hui-Chen Lu4¤, Christina Thaller2, Mei Xu5,
Sarah L. Pallas5, Michael C. Crair4, Joe Warren3, Wah Chiu1,2, Gregor Eichele6
1Program in Structural and Computational Biology and Molecular Biophysics, National Center for Macromolecular Imaging, 2Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America. 3Department of Computer Science, Rice University, Houston, Texas, United States of America. 4Division of Neuroscience and Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America. 5Department of Biology, Georgia State University, Atlanta, Georgia, United States of America. 6Max Planck Institute of Experimental Endocrinology, Hanover, Germany. Massive amounts of data are being generated in an effort to represent for the
brain the expression of all genes at cellular resolution. Critical to exploiting this
effort is the ability to place this data into a common frame of reference. Here we
have developed a computational method for annotating gene expression patterns
in the context of a digital atlas to facilitate custom user-queries and comparisons
of this type of data. This procedure has been applied to 200 genes in the
postnatal mouse brain. As an illustration of utility, we identify candidate genes
that may be related to Parkinson’s disease by using the expression of a
dopamine transporter in the substantia nigra as a search query pattern. In
addition, we discover that transcription factor Rorb is down-regulated in the
barrelless mutant relative to control mice by quantitative comparison of
expression patterns in layer IV somatosensory cortex. The semi-automated
annotation method developed here is applicable to a broad spectrum of complex
tissues and data modalities.
* To whom correspondence should be addressed. E-mail: [email protected]
¤ Current address: The Cain Foundation Laboratories, Department of Pediatrics, Division of Neuroscience and Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America.
Carson et al. A Digital Atlas for the Mouse Brain Transcriptome
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Synopsis
The mammalian brain is a complex organ with hundreds of functional parts. Describing
when and where genes are expressed in the brain is thus a potentially powerful method
for understanding the function of gene products. In recent years, several mammalian
genomes including human and mouse have been characterized. There are now efforts
around the world that aim to determine the expression patterns for all genes in the mouse
brain. To search this expression data readily, it must be placed into an atlas.
The authors propose a new method for bringing such genetic data into a common spatial
framework so that one can perform spatial searches and comparisons of gene expression
patterns. To create this atlas, the authors developed a series of maps of the brain using a
graphical modeling method called subdivision. These maps were deformed to match the
shape of tissue sections, and genetic activity information was associated with the
appropriate coordinates on the map.
After placing 200 genes into the context of this atlas, the authors illustrate its application
in discovering genes potentially involved in diseases and brain development.
Introduction
High-resolution maps of gene expression provide important information about
how genes regulate biological processes at cellular and molecular levels. Therefore a
multitude of efforts are in progress to depict gene expression at single cell resolution in
specimens ranging from organs to embryos (http://mamep.molgen.mpg.de[1];
Carson et al. A Digital Atlas for the Mouse Brain Transcriptome
Relative quantification of Rorb expression was performed with 18S rRNA as an
endogenous control. Each sample was run in triplicate to reduce pipetting error and
Carson et al. A Digital Atlas for the Mouse Brain Transcriptome
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increase consistency of the results. PCR was carried out at 50°C for 2min, 95°C for
10min, followed by 40 cycles of 95°C for 15sec and 60°C for 1 min. The expected size
of the PCR products was confirmed by gel electrophoresis. In addition, a conventional
PCR omitting the hybridization probe was run in parallel on a thermocycler to verify
PCR specificity. Equal amplification efficiency of Rorb to 18S rRNA was achieved,
validating the relative quantification.
Animals. C57BL/6 wild type mice from Jackson Laboratories were the source of
the line of mice used for all 200 genes. The discovery of brl mice resulted from a
spontaneous mutation in a line from ICR stock at Université de Lausanne[39]. Brl mice
used in our experiments were from the eighth backcross generation of the incipient
C57BL/6J-brl congenic inbred strain. Genotypes were determined by genomic PCR as
described[38]. Data analysis was performed blind to genotype. All animals were treated
in compliance with the guidelines of both the U.S. Department of Health and Human
Services and Baylor College of Medicine’s Animal Care and Use Committee.
Supporting Information
Figure S1. The subdivision-based anatomical atlas of the postnatal mouse brain
11 sagittal maps comprise this subdivision-based postnatal mouse brain atlas. The 15
major anatomical structures are color-coded as indicated by the labels.
Figure S2. Subdivision mesh
(A) An initial coarse mesh (left). The two transformations of subdivision: bi-linear
subdivision (middle) and then centroid averaging (right). (B) The mesh subdivided twice
(left), thrice (middle), and four times (right).
Carson et al. A Digital Atlas for the Mouse Brain Transcriptome
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Table S1. List of 200 riboprobes used.
Acknowledgments
We thank G. Alvarez-Bolado, M. Chen, A. Liang, A. Visel, and M. Yaylaoglu for
technical assistance, and D. Armstrong, M. Bello, I. Kakadiaris, and J. Maunsell for
advice and discussions. This research was supported by a fellowship (NLM Grant No.
5T15LM07093) from the Keck Center for Computational and Structural Biology of the
Gulf Coast Consortia, the Burroughs Welcome Fund, National Institutes of Health
(P41RR02250; EY-12696; R01 MH62639; F32 NS11034) and National Science
Foundation (IBN-0078110; EIA-0325004).
Conflicts of Interest. The authors have declared that no conflicts of interest exist.
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Figure 1. Postnatal day 7 (P7) mouse brain atlas construction and application
(A) Standard Nissl-stained P7 sagittal standard section number 4 with major anatomical